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- PDB-8tfh: Ricin in complex with Fab JB4 -

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Basic information

Entry
Database: PDB / ID: 8tfh
TitleRicin in complex with Fab JB4
Components
  • (JB4 monoclonal antibody ...) x 2
  • Ricin A chain
  • Ricin B chain
KeywordsTOXIN/IMMUNE SYSTEM / Ricin toxin / Fab / TOXIN / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil ...Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Ricinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: Biochemistry / Year: 2023
Title: Structural Basis of Antibody-Mediated Inhibition of Ricin Toxin Attachment to Host Cells.
Authors: Vance, D.J. / Rudolph, M.J. / Davis, S.A. / Mantis, N.J.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
B: Ricin B chain
H: JB4 monoclonal antibody heavy chain
L: JB4 monoclonal antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,79015
Polymers105,5614
Non-polymers2,22811
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.358, 139.358, 444.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ricin A chain / rRNA N-glycosidase


Mass: 29129.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase
#2: Protein Ricin B chain


Mass: 28989.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Lectin binds Gal/GalNac / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase

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Antibody , 2 types, 2 molecules HL

#3: Antibody JB4 monoclonal antibody heavy chain


Mass: 24160.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody JB4 monoclonal antibody light chain


Mass: 23280.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 3 molecules

#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 26 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.11 Å3/Da / Density % sol: 75.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5 M ammonium sulfate and 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. obs: 32952 / % possible obs: 97.4 % / Redundancy: 7.5 % / CC1/2: 0.44 / Net I/σ(I): 1.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.3-3.3661.83815900.2980.6780.7551.9950.99496.8
3.36-3.426.32.60915980.3290.7041.0512.8241.01896
3.42-3.486.35.73116210.3880.7472.2586.1861.02797.4
3.48-3.556.63.41515980.3770.741.3063.6720.99596.8
3.55-3.636.91.35915950.5450.840.5051.4561.0696.4
3.63-3.726.90.87916010.5950.8640.3210.941.77595.8
3.72-3.8170.93615880.6260.8780.3350.9981.73295.5
3.81-3.9175.03216030.6940.9051.8375.381.09496.5
3.91-4.0370.115960.7550.9280.10.11.24394.9
4.03-4.166.95.61516030.8030.9442.0616.0081.34496
4.16-4.316.71.01616060.8640.9630.3771.0881.43795.4
4.31-4.486.50.47616310.8450.9570.1760.5091.37197
4.48-4.686.50.92116380.9020.9740.3530.991.44397.3
4.68-4.936.50.84116550.9150.9780.3280.9071.2398.9
4.93-5.246.80.62216910.9080.9760.2450.6711.14199.8
5.24-5.647.50.51617060.9110.9760.1970.5541.1599.9
5.64-6.2190.4817050.9050.9750.1680.5091.089100
6.21-7.110.50.42717360.9260.9810.1370.451.115100
7.1-8.9411.50.23417570.9850.9960.0720.2451.226100
8.94-5011.20.118340.9970.9990.0310.1051.0398

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→33.84 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.334 1613 4.94 %
Rwork0.2739 --
obs0.2768 32671 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 141 18 7587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.815
X-RAY DIFFRACTIONf_dihedral_angle_d7.61129
X-RAY DIFFRACTIONf_chiral_restr0.0491200
X-RAY DIFFRACTIONf_plane_restr0.0061355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.380.41971140.35752485X-RAY DIFFRACTION94
3.39-3.490.45581370.35562523X-RAY DIFFRACTION96
3.49-3.620.33581140.32522558X-RAY DIFFRACTION97
3.62-3.760.38651450.31792531X-RAY DIFFRACTION96
3.76-3.930.45521160.34552491X-RAY DIFFRACTION94
3.93-4.140.40721360.33662420X-RAY DIFFRACTION92
4.14-4.40.35691280.27792544X-RAY DIFFRACTION95
4.4-4.740.30911340.26912550X-RAY DIFFRACTION95
4.74-5.210.32781480.24452652X-RAY DIFFRACTION99
5.22-5.970.27261490.22462689X-RAY DIFFRACTION100
5.97-7.50.28861550.24692725X-RAY DIFFRACTION100
7.5-33.840.24971370.2032890X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0864-1.3708-0.79411.90950.08992.2234-0.20981.2594-0.1348-0.75830.17860.6281-0.1063-0.1923-0.06560.8286-0.1485-0.30270.69530.29170.6472-147.9568-38.092-95.7824
20.8512-0.4011-2.35226.4456-0.06746.97870.12090.75650.8165-0.9942-0.78360.6832-0.7266-1.40190.00810.8965-0.0619-0.35240.91850.78810.9346-154.6164-23.9228-100.0443
32.7818-1.88740.97653.8304-0.31954.8045-0.2271-0.3576-0.17460.41990.41091.1783-0.9955-0.82060.01180.7257-0.003-0.33830.88220.41530.926-162.2733-30.7739-87.2197
45.8807-0.59675.19663.03571.61396.15310.82230.1462-0.49250.6750.35590.19271.303-1.5039-1.04970.8044-0.0859-0.12950.87060.36140.7245-156.1275-43.1674-79.2663
53.38780.7805-0.78723.4504-0.44774.8660.34570.31180.4223-0.7568-0.08180.0433-0.0838-0.7865-0.21530.72550.147-0.11180.38980.17490.6483-141.1115-30.7019-75.0298
62.67381.5830.5095.3652-2.72342.3779-0.19330.76970.71620.08660.1093-0.2441-0.75220.15460.06770.44280.0597-0.07780.59920.22790.495-136.1925-33.0149-78.6266
71.92010.0858-0.82043.2290.7362.7601-0.0089-0.19160.221-0.25930.2309-0.06-0.6666-0.5427-0.2310.48990.0198-0.08950.3965-0.01480.4944-121.904-32.7168-61.2284
83.576-0.60991.34660.9681.54386.91940.01540.23260.3635-0.2581-0.045-0.1995-0.18840.691-0.01040.4744-0.06710.05660.3403-0.00460.4226-114.1533-37.1046-67.5642
91.96152.096-0.16583.1020.67991.424-0.4537-0.27750.0804-0.10110.520.2653-0.1124-0.1662-0.12350.73120.075-0.04660.28110.04980.3554-129.3514-44.3896-67.0935
105.33140.4241.93296.14260.59476.6423-0.3115-0.3087-0.43080.43470.30670.96271.3691-1.36050.18990.5929-0.30970.1030.62660.2250.767-147.8526-58.2244-68.647
114.10824.32413.28874.56782.92236.2753-0.2605-0.91090.32671.05960.11880.69550.5870.27220.36010.60360.12180.09480.38660.18240.7269-144.0027-49.2498-63.8297
124.4251-1.1736-0.59384.84994.23655.5822-0.239-0.5022-0.180.26410.4486-0.55770.81170.1303-0.25050.47220.01880.06320.4450.23270.4145-134.8262-57.3678-65.9469
134.25480.3865-0.35595.92760.87871.5388-0.24240.5307-0.3623-0.33520.4397-0.2370.26450.0755-0.0710.4572-0.1805-0.04640.40270.18790.5459-137.3057-55.9167-75.015
143.5789-2.3292-2.50715.56242.61781.99730.78940.7213-0.39220.59620.23860.20822.90191.5648-0.88430.56790.11790.00620.6637-0.26990.6215-90.6174-57.5378-86.7729
156.45410.3698-0.52292.74990.64185.17840.22130.7938-0.8365-0.3302-0.13730.5596-0.00380.1495-0.07880.45860.03230.02620.4309-0.17690.5121-98.3693-51.0681-83.603
162.883-1.14230.95952.8238-0.76410.3798-0.4415-0.806-1.7210.51650.1060.3793-0.34520.26670.1850.4320.04320.17310.8506-0.29310.2965-94.6456-45.4032-73.3125
172.6632-2.084-2.14972.35091.06922.04510.14610.5713-0.3674-0.2311-0.77830.1956-0.096-0.34610.5960.4223-0.08740.08190.7571-0.18780.6471-81.3076-56.4494-91.2997
188.56851.8836-0.88356.5396-0.8467.3386-0.0299-0.3674-2.67680.20860.2346-0.9728-0.30161.5855-0.21680.5856-0.22670.18971.0078-0.10160.9097-56.2833-55.7008-93.3414
192.2019-2.22952.01122.3565-1.77611.9646-0.776-0.9755-0.38411.05440.6654-0.0246-1.08480.05140.06710.4711-0.12740.12861.04150.04340.6164-69.9202-58.1359-87.0193
208.9288-3.60334.3518.9675-3.45682.64050.7760.48951.4538-1.2396-0.536-0.62710.18070.8960.11070.4614-0.02710.28880.9024-0.19380.6716-68.6736-52.8349-94.9984
213.41231.2313-0.6263.0863-1.03592.18970.2993-1.3421-0.32220.2818-0.4955-0.74570.7576-0.6006-0.50370.623-0.414-0.12291.0009-0.20320.86-59.0301-62.2766-85.8983
222.108-0.57452.19242.62240.46746.46321.0565-0.885-0.6257-0.5901-1.0959-0.24910.32480.09710.04940.7997-0.0724-0.16070.7812-0.03810.7724-64.8872-65.7012-92.6103
236.2367-0.087-2.88413.1225-0.4333.2424-0.52291.34160.2516-0.77220.918-0.5747-0.25150.3253-0.5810.5928-0.05990.4030.6555-0.28380.5566-86.1998-32.3681-78.5078
244.2809-0.0558-1.64511.49110.5142.51070.04-0.1310.4711-0.11450.2894-0.2218-0.39310.6035-0.23520.5565-0.12010.11840.4546-0.03850.4896-78.9519-35.395-79.0142
253.289-1.02060.55042.68191.38221.9939-0.07880.2134-0.0404-0.84420.1875-0.5566-0.74540.4827-0.18690.8167-0.02270.52430.9073-0.21070.9203-59.4702-47.0251-101.6516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 263 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 47 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 118 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 146 )
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 163 )
11X-RAY DIFFRACTION11chain 'B' and (resid 164 through 180 )
12X-RAY DIFFRACTION12chain 'B' and (resid 181 through 202 )
13X-RAY DIFFRACTION13chain 'B' and (resid 203 through 262 )
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 17 )
15X-RAY DIFFRACTION15chain 'H' and (resid 18 through 91 )
16X-RAY DIFFRACTION16chain 'H' and (resid 92 through 108 )
17X-RAY DIFFRACTION17chain 'H' and (resid 109 through 133 )
18X-RAY DIFFRACTION18chain 'H' and (resid 134 through 154 )
19X-RAY DIFFRACTION19chain 'H' and (resid 155 through 171 )
20X-RAY DIFFRACTION20chain 'H' and (resid 172 through 193 )
21X-RAY DIFFRACTION21chain 'H' and (resid 194 through 208 )
22X-RAY DIFFRACTION22chain 'H' and (resid 209 through 223 )
23X-RAY DIFFRACTION23chain 'L' and (resid 1 through 49 )
24X-RAY DIFFRACTION24chain 'L' and (resid 50 through 120 )
25X-RAY DIFFRACTION25chain 'L' and (resid 121 through 210 )

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